Personally I always found the later movies more disappointing than individual TV episodes. You could argue that having more money thrown at them made them forget about things like "script" & "plot" in favour of the Enterprise being destroyed (again).
Individual episodes could be bad, but at least there was always another one to see to get over it.
For missed opportunities:
More 'alternate view' episodes. Some of the episodes I enjoyed the most were not featuring the main crew, such as in "Lower Decks". What I also enjoyed in that episode was the death of one of them. Unlike the original series, no-one ever appears to die in subsequent ST franchises or at least very, very rarely. I think in such a dangerous job you have to treat your audience with a bit more respect otherwise it's just a "ho-hum, what ludicrious way will they escape unscathed this time?" situation.
Less "holodeck goes horribly wrong" episodes. It seemed every season this happened at least once. In the real world, Health and Safety would ensure these were decommissioned and never used again
More 'no-win' episodes. It slightly annoyed me that every time the Enterprise encountered a problem, it was inevitably solved at the last minute and everyone went away happily ever after. Only a few "The Masterpiece Society" & "The Defector" ever really explored the idea that there can be instances where the only result is negative.
And finally, a few more actual "science" in star trek. The episode where the Enterprise encountered a Dyson Sphere was a good/bad one as they never explored it! It was merely a plot device for Scotty's return. I would have enjoyed a few more stories theorising about current science 'what-ifs'.
Having said all this, I thought Star Trek was a damned good franchise with good episodes in all the incarnations. Enterprise died on it's backside because, IMO, the time wasn't right for another starship-based adventure. I think that was part of the reason for DS9's fresh feel, although they also sadly regressed into a starship-based series towards the end.